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- PDB-3w1j: Crystal structure of the N-terminal truncated selenocysteine synt... -

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Basic information

Entry
Database: PDB / ID: 3w1j
TitleCrystal structure of the N-terminal truncated selenocysteine synthase SelA in complex with thiosulfate
ComponentsL-seryl-tRNA(Sec) selenium transferase
KeywordsTRANSFERASE / homodecamer / pentamer of dimers / fold-type I pyridoxal 5'-phosphate (PLP) dependent enzyme / L-seryl-tRNA(Sec) selenium transferase / selenocysteine synthesis / selenium metabolism
Function / homology
Function and homology information


L-seryl-tRNASec selenium transferase / L-seryl-tRNA(Sec) selenium transferase activity / conversion of seryl-tRNAsec to selenocys-tRNAsec / selenocysteine incorporation / identical protein binding / cytoplasm
Similarity search - Function
Aspartate Aminotransferase, domain 1 - #180 / L-seryl-tRNA(Sec) selenium transferase / L-seryl-tRNA selenium transferase-like / L-seryl-tRNA selenium transferase / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase; domain 2 / Type I PLP-dependent aspartate aminotransferase-like (Major domain) / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase / Alpha-Beta Complex ...Aspartate Aminotransferase, domain 1 - #180 / L-seryl-tRNA(Sec) selenium transferase / L-seryl-tRNA selenium transferase-like / L-seryl-tRNA selenium transferase / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase; domain 2 / Type I PLP-dependent aspartate aminotransferase-like (Major domain) / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase / Alpha-Beta Complex / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
: / THIOSULFATE / L-seryl-tRNA(Sec) selenium transferase
Similarity search - Component
Biological speciesAquifex aeolicus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.252 Å
AuthorsItoh, Y. / Sekine, S. / Yokoyama, S.
CitationJournal: Science / Year: 2013
Title: Decameric SelA-tRNA(Sec) ring structure reveals mechanism of bacterial selenocysteine formation
Authors: Itoh, Y. / Brocker, M.J. / Sekine, S. / Hammond, G. / Suetsugu, S. / Soll, D. / Yokoyama, S.
History
DepositionNov 15, 2012Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 5, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Refinement description / Category: software
Revision 1.2Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: L-seryl-tRNA(Sec) selenium transferase
B: L-seryl-tRNA(Sec) selenium transferase
C: L-seryl-tRNA(Sec) selenium transferase
D: L-seryl-tRNA(Sec) selenium transferase
E: L-seryl-tRNA(Sec) selenium transferase
F: L-seryl-tRNA(Sec) selenium transferase
G: L-seryl-tRNA(Sec) selenium transferase
H: L-seryl-tRNA(Sec) selenium transferase
I: L-seryl-tRNA(Sec) selenium transferase
J: L-seryl-tRNA(Sec) selenium transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)441,97131
Polymers439,98110
Non-polymers1,99021
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area56560 Å2
ΔGint-214 kcal/mol
Surface area145750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.442, 116.372, 124.788
Angle α, β, γ (deg.)102.090, 93.390, 106.060
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
L-seryl-tRNA(Sec) selenium transferase / Selenocysteine synthase / Sec synthase / Selenocysteinyl-tRNA(Sec) synthase


Mass: 43998.105 Da / Num. of mol.: 10
Fragment: the core and C-terminal domains, UNP residues 62-452
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aquifex aeolicus (bacteria) / Strain: VF5 / Gene: selA / Plasmid: pET22b / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta 2(DE3)
References: UniProt: O67140, L-seryl-tRNASec selenium transferase
#2: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: K
#3: Chemical
ChemComp-THJ / THIOSULFATE


Mass: 112.128 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: O3S2

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.84 Å3/Da / Density % sol: 56.76 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 120mM Tris-HCl, 12% PEG 4000, 800mM NaNO3, 160mM KCl, 50mM L-serine, 50mM Na2S2O3, 0.2M NaCl, 10mM 2-mercaptoethanol, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: May 31, 2007 / Details: mirrors
RadiationMonochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.25→50 Å / Num. all: 76007 / Num. obs: 75475 / % possible obs: 99.3 % / Observed criterion σ(I): -2 / Redundancy: 3.9 % / Rmerge(I) obs: 0.129 / Rsym value: 0.129 / Net I/σ(I): 12.7
Reflection shellResolution: 3.25→3.37 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.538 / Mean I/σ(I) obs: 2.05 / Rsym value: 0.538 / % possible all: 98.6

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
PHENIX1.7.1_743refinement
PDB_EXTRACT3.11data extraction
ADSCQuantumdata collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3W1I

3w1i


Resolution: 3.252→38.518 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.753 / SU ML: 0.92 / σ(F): 1.97 / Phase error: 31.28 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2661 3812 5.06 %RANDOM
Rwork0.2003 ---
obs0.2036 75371 98.94 %-
all-76178 --
Solvent computationShrinkage radii: 0.16 Å / VDW probe radii: 0.5 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 70.465 Å2 / ksol: 0.285 e/Å3
Displacement parametersBiso max: 333.29 Å2 / Biso mean: 123.2922 Å2 / Biso min: 41.21 Å2
Baniso -1Baniso -2Baniso -3
1--40.2921 Å2-0.5608 Å2-7.5529 Å2
2--41.1022 Å2-2.4413 Å2
3----0.8101 Å2
Refinement stepCycle: LAST / Resolution: 3.252→38.518 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms30803 0 85 0 30888
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00931277
X-RAY DIFFRACTIONf_angle_d1.2642075
X-RAY DIFFRACTIONf_chiral_restr0.0744853
X-RAY DIFFRACTIONf_plane_restr0.0045333
X-RAY DIFFRACTIONf_dihedral_angle_d14.10912151
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 27

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.2523-3.29340.43921380.33992501263992
3.2934-3.33670.36131310.3162631276299
3.3367-3.38240.38141670.29732624279199
3.3824-3.43070.34671250.26342699282499
3.4307-3.48190.31841300.26562591272199
3.4819-3.53630.34131480.25582711285999
3.5363-3.59420.30971300.24982597272799
3.5942-3.65610.29581310.23222689282099
3.6561-3.72260.31731440.2332652279699
3.7226-3.79410.31961400.22782635277599
3.7941-3.87150.27061560.21622668282499
3.8715-3.95560.25341440.20422628277299
3.9556-4.04750.271280.19382654278299
4.0475-4.14860.23661460.18182652279899
4.1486-4.26060.2621490.17852637278699
4.2606-4.38580.26121410.16642691283299
4.3858-4.52720.21771350.15932653278899
4.5272-4.68870.22451340.14932695282999
4.6887-4.87610.22981320.14832670280299
4.8761-5.09750.2531520.158326402792100
5.0975-5.36560.23091380.165826772815100
5.3656-5.70080.30421520.199826492801100
5.7008-6.13930.29751340.203226882822100
6.1393-6.75420.31481590.227826372796100
6.7542-7.72470.26041550.179426722827100
7.7247-9.70650.18161400.143526722812100
9.7065-38.52090.24531330.24292646277999
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.1835-0.3473-0.03530.7774-0.0352.1292-0.3230.3029-0.2329-0.140.1114-0.0988-0.0011-0.00420.20260.81110.01-0.04730.5052-0.02070.937542.121-36.232929.4896
21.82980.0297-0.33911.92020.91083.1408-0.0607-0.0922-0.44560.0967-0.01950.02450.3181-0.41070.09230.668-0.06610.09040.4191-0.06550.590721.2751-36.547445.9671
32.6605-0.5953-1.54281.3369-1.33273.3137-0.209-0.4191-0.16950.1304-0.2643-0.40320.37040.70250.45570.8160.01230.01860.62250.0581.011754.7537-43.16438.5309
43.13540.6244-0.57043.6680.22851.96990.10570.1673-0.8463-0.75480.05540.04880.3957-0.0058-0.15051.0071-0.1947-0.0030.8883-0.32170.892716.3364-48.740721.2634
53.221-1.35770.16822.9068-1.08641.6014-0.02150.3276-0.0171-0.19110.082-0.15570.3058-0.316-0.06880.5965-0.05470.0520.5981-0.18620.467120.6064-23.401719.7771
60.81730.2317-0.30752.37820.13741.20480.12180.4694-0.7928-0.80990.28170.28941.1858-0.3559-0.30621.4357-0.3233-0.22471.2391-0.34961.2699.9788-54.08058.3106
73.6872-1.39150.12182.6585-1.38395.65640.48561.15180.2355-0.033-0.2898-0.4191-0.33141.7336-0.14280.7627-0.17470.0171.9029-0.19491.1229-17.8435-11.9584-8.3152
83.6551-0.54550.62451.2931-0.55581.8486-0.0430.8491-0.3357-0.19790.0560.0990.06340.2378-0.02220.5321-0.0830.03440.7792-0.07060.5467-22.7625-20.023716.6243
91.3685-0.54770.23382.8662-0.35153.5770.13711.3887-0.0882-1.3142-0.0764-0.33720.33550.6459-0.13861.1069-0.03230.06022.4072-0.31571.0795-12.936-25.9429-16.1459
103.7094-1.1715-0.02512.0366-1.17193.22660.02371.32590.0145-0.0216-0.647-0.4314-0.13250.31840.47460.7341-0.10060.03961.35810.22170.7292-44.1188-6.68845.1026
111.47450.70010.30512.08751.10951.7597-0.10050.95550.4663-0.31840.2425-0.0947-0.37970.2789-0.11670.6352-0.18170.02731.19460.36060.7993-23.62368.12318.4334
122.07231.10180.60072.0361-0.86051.1885-0.26880.73760.7944-0.3860.11560.298-0.1697-0.0813-0.04440.8508-0.1768-0.0681.40070.40010.9026-56.91081.87070.9477
132.27950.9988-1.23443.5972-1.51022.3940.2519-0.20890.6933-0.3665-0.1539-0.1019-0.3479-0.00690.01041.0870.0175-0.30980.84540.28581.593-46.754145.351428.2191
141.5633-0.3984-0.10352.38771.24571.1873-0.0637-0.1060.18230.1782-0.03150.51820.1781-0.20760.11550.787-0.02660.06230.70680.34241.1808-46.289823.066542.3976
151.2962-0.21360.2342.0331-0.58762.1346-0.03130.72940.67-0.662-0.32270.4782-0.6651-0.20030.25881.15810.0954-0.36791.13760.3331.7557-56.499241.394715.0875
162.7304-0.6878-1.27881.1882-0.48123.7314-0.7106-0.7561-0.0703-0.20520.37290.2431-0.03130.35780.36811.19810.0050.08461.6285-0.13812.106-54.319343.739557.5214
172.84630.24211.3441.2650.14162.3065-0.13110.09290.6449-0.01010.01160.3466-0.4467-0.05740.1010.8212-0.00990.03050.55280.19261.0927-29.410545.9848.625
182.85010.2372-0.67730.97960.21960.87440.194-0.98610.95910.6904-0.15680.6284-0.1834-0.7096-0.05741.3364-0.06440.29551.719-0.24172.1361-56.277657.046167.7588
194.8682-0.73780.35933.78450.22464.2514-1.0782-0.42310.8709-0.0613-0.15440.6834-0.86340.00921.2121.55850.5294-0.40921.1147-0.18161.891-9.011556.275791.9793
202.7477-0.18510.63142.83890.95223.0886-0.3407-0.62890.24210.8550.53660.36220.0086-0.503-0.23741.20160.24830.17470.69260.07950.9574-17.895832.805188.8092
212.08351.24450.13922.07320.79740.9629-0.5191-0.47472.0218-0.00440.25271.1394-0.70430.13530.35391.89240.3263-0.21791.3094-0.27512.523-19.850267.291192.9865
222.80193.0036-1.13674.595-1.88513.80910.0797-0.33610.78450.4170.72060.56170.1803-0.3661-0.77451.90530.8132-0.22941.4271-0.25841.1473-0.766433.0874109.3082
232.6361-0.4193-0.56711.93451.36792.5915-0.4515-0.10850.89540.63970.4057-0.2656-0.47920.27080.04891.22460.1084-0.21040.5966-0.09811.008310.904737.425986.1352
241.40760.6931-0.33571.0287-0.89552.5336-0.0898-0.81190.20530.85620.33390.0473-0.73810.0022-0.15282.34190.6623-0.22891.257-0.28361.150712.184431.9963120.2965
253.04610.0318-1.25212.2620.01243.2537-0.8622-0.86590.75810.73620.4911-0.70290.6-0.05080.23451.230.2217-0.18351.3916-0.34450.818347.97146.614591.1922
264.4732-0.60480.5061.74680.0031.7502-0.1339-1.1264-0.03260.56210.08630.2179-0.0952-0.20150.05391.14290.14990.05640.6927-0.00890.456323.6312-4.030190.6249
272.9080.78820.09890.61660.28850.952-0.0892-1.44821.24020.69650.1743-0.307-0.61680.69750.01741.72730.0984-0.2471.7162-0.54421.331348.596114.1431106.3867
283.77081.84930.05423.3627-1.51492.17680.5531-0.85020.44960.3842-0.22670.2160.3361-0.022-0.21261.18960.262-0.04140.7825-0.06090.631742.4111-22.903587.1029
293.2760.06140.7181.1890.30463.3117-0.14880.08610.36010.03490.0075-0.1602-0.46470.31820.12180.84590.02220.04060.33510.04030.489541.9861-5.059167.785
301.1877-0.36280.32991.6256-0.87642.1476-0.0992-0.2337-1.03410.34570.1024-0.45691.23180.76530.0261.39430.4386-0.06941.16810.13151.227753.8945-34.226281.9465
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1CHAIN A AND (RESSEQ 61:89)A61 - 89
2X-RAY DIFFRACTION2CHAIN A AND (RESSEQ 90:338)A90 - 338
3X-RAY DIFFRACTION3CHAIN A AND (RESSEQ 339:452)A339 - 452
4X-RAY DIFFRACTION4CHAIN B AND (RESSEQ 63:89)B63 - 89
5X-RAY DIFFRACTION5CHAIN B AND (RESSEQ 90:338)B90 - 338
6X-RAY DIFFRACTION6CHAIN B AND (RESSEQ 339:452)B339 - 452
7X-RAY DIFFRACTION7CHAIN C AND (RESSEQ 61:89)C61 - 89
8X-RAY DIFFRACTION8CHAIN C AND (RESSEQ 90:338)C90 - 338
9X-RAY DIFFRACTION9CHAIN C AND (RESSEQ 339:452)C339 - 452
10X-RAY DIFFRACTION10CHAIN D AND (RESSEQ 63:89)D63 - 89
11X-RAY DIFFRACTION11CHAIN D AND (RESSEQ 90:338)D90 - 338
12X-RAY DIFFRACTION12CHAIN D AND (RESSEQ 339:452)D339 - 452
13X-RAY DIFFRACTION13CHAIN E AND (RESSEQ 61:89)E61 - 89
14X-RAY DIFFRACTION14CHAIN E AND (RESSEQ 90:338)E90 - 338
15X-RAY DIFFRACTION15CHAIN E AND (RESSEQ 339:452)E339 - 452
16X-RAY DIFFRACTION16CHAIN F AND (RESSEQ 61:89)F61 - 89
17X-RAY DIFFRACTION17CHAIN F AND (RESSEQ 90:338)F90 - 338
18X-RAY DIFFRACTION18CHAIN F AND (RESSEQ 339:452)F339 - 452
19X-RAY DIFFRACTION19CHAIN G AND (RESSEQ 64:89)G64 - 89
20X-RAY DIFFRACTION20CHAIN G AND (RESSEQ 90:338)G90 - 338
21X-RAY DIFFRACTION21CHAIN G AND (RESSEQ 339:452)G339 - 452
22X-RAY DIFFRACTION22CHAIN H AND (RESSEQ 61:89)H61 - 89
23X-RAY DIFFRACTION23CHAIN H AND (RESSEQ 90:338)H90 - 338
24X-RAY DIFFRACTION24CHAIN H AND (RESSEQ 339:452)H339 - 452
25X-RAY DIFFRACTION25CHAIN I AND (RESSEQ 61:89)I61 - 89
26X-RAY DIFFRACTION26CHAIN I AND (RESSEQ 90:338)I90 - 338
27X-RAY DIFFRACTION27CHAIN I AND (RESSEQ 339:452)I339 - 452
28X-RAY DIFFRACTION28CHAIN J AND (RESSEQ 61:89)J61 - 89
29X-RAY DIFFRACTION29CHAIN J AND (RESSEQ 90:338)J90 - 338
30X-RAY DIFFRACTION30CHAIN J AND (RESSEQ 339:452)J339 - 452

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